WSMO-lite annotations for web services

and other research output

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies

Semantic web service automation with lightweight annotations

Web services, both RESTful and WSDL-based, are an increasingly important part of the Web. With the application of semantic technologies, we can achieve automation of the use of those services. In this paper, we present WSMO-Lite and MicroWSMO, two related lightweight approaches to semantic Web service description, evolved from the WSMO framework. WSMO-Lite uses SAWSDL to annotate WSDL-based services, whereas MicroWSMO uses the hRESTS microformat to annotate RESTful APIs and services. Both frameworks share an ontology for service semantics together with most of automation algorithms

Grounding semantic web services with rules

Semantic web services achieve effects in the world through web services, so the connection to those services - the grounding - is of paramount importance. The established technique is to use XML-based translations between ontologies and the SOAP message formats of the services, but these mappings cannot address the growing number of non-SOAP services, and step outside the ontological world to describe the mapping. We present an approach which draws the service's interface into the ontology: we define ontology objects which represent the whole HTTP message, and use backward-chaining rules to translate between semantic service invocation instances and the HTTP messages passed to and from the service. We present a case study using Amazon's popular Simple Storage Service

XQOWL: An Extension of XQuery for OWL Querying and Reasoning

One of the main aims of the so-called Web of Data is to be able to handle heterogeneous resources where data can be expressed in either XML or RDF. The design of programming languages able to handle both XML and RDF data is a key target in this context. In this paper we present a framework called XQOWL that makes possible to handle XML and RDF/OWL data with XQuery. XQOWL can be considered as an extension of the XQuery language that connects XQuery with SPARQL and OWL reasoners. XQOWL embeds SPARQL queries (via Jena SPARQL engine) in XQuery and enables to make calls to OWL reasoners (HermiT, Pellet and FaCT++) from XQuery. It permits to combine queries against XML and RDF/OWL resources as well as to reason with RDF/OWL data. Therefore input data can be either XML or RDF/OWL and output data can be formatted in XML (also using RDF/OWL XML serialization).Comment: In Proceedings PROLE 2014, arXiv:1501.0169

Semantically Resolving Type Mismatches in Scientific Workflows

Scientists are increasingly utilizing Grids to manage large data sets and execute scientific experiments on distributed resources. Scientific workflows are used as means for modeling and enacting scientific experiments. Windows Workflow Foundation (WF) is a major component of Microsoft’s .NET technology which offers lightweight support for long-running workflows. It provides a comfortable graphical and programmatic environment for the development of extended BPEL-style workflows. WF’s visual features ease the syntactic composition of Web services into scientific workflows but do nothing to assure that information passed between services has consistent semantic types or representations or that deviant flows, errors and compensations are handled meaningfully. In this paper we introduce SAWSDL-compliant annotations for WF and use them with a semantic reasoner to guarantee semantic type correctness in scientific workflows. Examples from bioinformatics are presented

Data mediation to message level conflict in heterogeneous web services

Enterprise Information Systems (EISs) are built in isolated and independent environments leading to unpredictable and incompatible structure of data stores. An EI system can expose its functionalities as Web services to share resources of existing global internet infrastructure. The goal of this research paper is to facilitate inter-operation between Web services. Successful and reliable information (message) exchange between Web services is necessary to meet the current challenge of Enterprise Information Integration (EII). A real-\ud world business process, which consists of Web services WS1 and WS2, can be used as a practical scenario for data or message exchange between Web services. In this scenario, message is exchanged by using output of WS1 as input of WS2. If data format of WS1 and WS2 are heterogeneous or incompatible, interoperation between them is impossible if data mediation is not used to resolve message level conflict and incompatibility in the context of syntax and semantics. Data Mediation requires mapping a message from one format to another. We propose to derive a mediation technique that will enable previously less inter-operative heterogeneous Web services to become more inter-operative now. To improve inter-operational performance between Web services our data mediation approach extends and utilizes existing Web service supporting tools WSDL and SAWSDL. (Authors' abstract